Lukasz Fabianski was the unlikely hero as Arsenal reached the Cup final the hard way, huffing and puffing over 120 minutes before finally beating Wigan Athletic on penalties. Little the Premier League side managed in open play was as convincing as the saves Fabianski made to deny first Gary Caldwell then Jack Collison from the spot – the goalkeeper who only appears in Cup competitions producing an athletic stop from the second penalty to leave Wigan with too great a deficit to recover. All the other penalties were scored, which meant Santi Cazorla put Arsenal through with his side's fourth kick.

Still hopeful of promotion through the Championship play-offs this season, Wigan deserved credit for taking Arsenal the full distance. While for a few minutes in the second half it appeared the holders might even reach a second successive final, they ended up with just the hollow consolation of putting up a better defence of last year's trophy than almost anyone could have predicted.

In normal time, Per Mertesacker was both hero and villain, giving away the penalty that briefly encouraged Wigan, then equalising nine minutes from the end to send the semi into extra time. The German defender clearly felt he had got some of the ball when he was adjudged to have fouled Callum McManaman after an hour, and when he was able to make amends at the other end his emotional reaction showed immense relief.

The relief for Arsenal was palpable too. For most of the game they had been sluggish and unimaginative, and until Mertesacker's equaliser looked perfectly capable of joining Manchester City, Crystal Palace and Cardiff City on Wigan's list of Premier League victims this season. Only when they went behind did Arsenal show the necessary fight to contest a semi-final – for the most part they made life quite comfortable for their Championship opponents.

Playing on the right, Alex Oxlade-Chamberlain showed up well for Arsenal in the opening stages, almost creating a goal after five minutes with a run and cross for Yaya Sanogo. The striker managed to keep his near-post header on target but Scott Carson reacted well in the Wigan goal. When Oxlade-Chamberlain beat Wigan's off-side trap in the 15th minute to get behind Stephen Crainey and stride into the penalty area Carson again reacted smartly, leaving his line to snuff out the danger.

It was already clear that much of the game would be played in the Wigan half, with McManaman rarely getting forward with the ball and even Marc-Antoine Fortuné, the Championship side's notional front man, retreating across the halfway line at times.

Bacary Sagna flashed a shot wide from a narrow angle following an Arsenal corner, then Jordi Gómez narrowly missed the target in an attempt to catch Fabianski off his line from a similarly unpromising position. By the half-hour stage, although still not mounting many attacks, Wigan were at least stroking the ball around with confidence and finding each other quite calmly, gradually feeling their way into the game. The semi-final did not look like an obvious mismatch between a Championship side and one with notional Champions League status, and by the time McManaman broke free to send a shot just over the bar shortly before the interval it was fair to say Wigan had withstood Arsenal's early pressure and begun to exert a little of their own. But three minutes before the break Podolski played Sanogo through on the left, but once again Carson was equal to the situation. Aided by a slightly heavy first touch from Sanogo that showed him too much of the ball, the goalkeeper was alert enough to come out and smother the eventual shot.

Arsenal badly needed to up the tempo for the second half and bring some of their pace to bear, if not some of their class. To judge by the frown on Arsène Wenger's face as he resumed his seat he might have spent the interval listening to Roy Keane's acerbic remarks on TV.

Not that the Arsenal manager was actually in his seat for long, he spent most of the game pacing his technical area with folded arms and a pensive expression.

Cazorla tried to play in Sanogo with a diagonal ball only for Ivan Ramis to block his run and allow Carson to gather, before Wenger's afternoon became infinitely worse on the hour when Mertesacker gave away a penalty. McManaman was merely trying his luck with a run into the area when the German stuck out a long leg and caught more of the man than the ball.

Michael Oliver had a good view and took a moment to consider his decision but concluded there had been contact and pointed to the spot. The spot-kick had to wait three minutes while Nacho Monreal received treatment on the right, the full-back eventually having to leave on a stretcher after becoming injured in the passage of play preceding McManaman's run, but Gómez coolly bided his time before beating Fabianski with the most assured of penalties.

Now Arsenal were forced to inject some urgency into their game, and they did. A good cover tackle by Crainey was needed to stop Sanogo in full flight, then Oxlade-Chamberlain saw a shot saved before a flurry of events led to the equaliser. Kieran Gibbs beat Carson with a diving header only to see Crainey clear off the line, then when the resulting corner was half-cleared, Oxlade-Chamberlain sent the ball back goalwards to find Mertesacker still in the penalty area and just on-side to score with a close-range header. The defender celebrated as if he had just won the Cup, not merely kept his side in it.

Extra time featured another fine save by Carson from Sanogo to keep the scores level, and a hooked shot over the bar by the same striker from the six-yard line when he should probably have done better.

Wigan kept plugging away, though another half-hour at Wembley is about the last thing a Championship side that began the season in the Europa League either wants or needs, and their resistance became increasingly token as energy ebbed away.

Oxlade-Chamberlain, still full of energy in the 110th minute, burst fiercely on to the ball and almost wrapped up the game with a fizzing drive from the edge of the area that struck the angle of post and crossbar, and though Wigan gamely tried to counter, Collison was well wide with a late header from Jean Beausejour's cross. With players beginning to cramp up, Wigan substitute Nick Powell was able to set off on a promising late run, yet missed the target by a distance when the hard work seemed done.

That proved to be the game's last chance from open play. Two tired teams seemed happy to settle for penalties.